Modelling process uncertainty

Sebastian Funk

5 July, 2019

Example: Ebola forecasting in 2014-16

The unknown

  • Community/hospital/funeral transmission
  • Spatial dynamics
  • Changes in behaviour
  • Changes in reporting
  • Interventions
  • Seasonality
  • etc

The known

  • Average incubation period (~9 days)
  • Average infectious period (~11 days)
  • Case-fatality rate (~70%)

WHO Ebola response team (2014)

Transmission intensity as a stochastic process

\(d\log(R_0(t)) = \sigma dW_t\)

Dureau (2013)

Particle MCMC

  • Method for filtering trajectories consistent with data
  • Highly parallelisable

Andrieu (2010), Murray (2013)

Particle filter to estimate posterior trajectories

Filtered trajectories tell us something about dynamics